@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/slice/index.js

@@ -1,46 +1,48 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _values = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/values"));
-
-var _promise = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/promise"));
-
-var _filter = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/filter"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _flags = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/flags"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _map = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/map"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var _context17;
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError,
-    CramBufferOverrunError = _require.CramBufferOverrunError,
-    CramArgumentError = _require.CramArgumentError;
-
-var _require2 = require('../util'),
-    parseItem = _require2.parseItem,
-    tinyMemoize = _require2.tinyMemoize,
-    sequenceMD5 = _require2.sequenceMD5;
-
-var Constants = require('../constants');
-
-var decodeRecord = require('./decodeRecord');
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var errors_1 = require("../../errors");
+var util_1 = require("../util");
+var constants_1 = __importDefault(require("../constants"));
+var decodeRecord_1 = __importDefault(require("./decodeRecord"));
 /**
  * @private
  * Try to estimate the template length from a bunch of interrelated multi-segment reads.
@@ -48,33 +50,30 @@ var decodeRecord = require('./decodeRecord');
  * @param {number} currentRecordNumber
  * @param {CramRecord} thisRecord
  */
-
-
 function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord) {
-  function getAllMatedRecords(startRecord) {
-    var records = [startRecord];
-
-    if (startRecord.mateRecordNumber >= 0) {
-      var mateRecord = allRecords[startRecord.mateRecordNumber];
-      if (!mateRecord) throw new CramMalformedError('intra-slice mate record not found, this file seems malformed');
-      records.push.apply(records, (0, _toConsumableArray2.default)(getAllMatedRecords(mateRecord)));
+    function getAllMatedRecords(startRecord) {
+        var records = [startRecord];
+        if (startRecord.mateRecordNumber >= 0) {
+            var mateRecord = allRecords[startRecord.mateRecordNumber];
+            if (!mateRecord) {
+                throw new errors_1.CramMalformedError('intra-slice mate record not found, this file seems malformed');
+            }
+            records.push.apply(records, getAllMatedRecords(mateRecord));
+        }
+        return records;
+    }
+    var matedRecords = getAllMatedRecords(thisRecord);
+    var starts = matedRecords.map(function (r) { return r.alignmentStart; });
+    var ends = matedRecords.map(function (r) { return r.alignmentStart + r.readLength - 1; });
+    var estimatedTemplateLength = Math.max.apply(Math, ends) - Math.min.apply(Math, starts) + 1;
+    if (estimatedTemplateLength >= 0) {
+        matedRecords.forEach(function (r) {
+            if (r.templateLength !== undefined) {
+                throw new errors_1.CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
+            }
+            r.templateLength = estimatedTemplateLength;
+        });
     }
-
-    return records;
-  }
-
-  var matedRecords = getAllMatedRecords(thisRecord);
-  var starts = (0, _map.default)(matedRecords).call(matedRecords, function (r) {
-    return r.alignmentStart;
-  });
-  var ends = (0, _map.default)(matedRecords).call(matedRecords, function (r) {
-    return r.alignmentStart + r.readLength - 1;
-  });
-  var estimatedTemplateLength = Math.max.apply(Math, (0, _toConsumableArray2.default)(ends)) - Math.min.apply(Math, (0, _toConsumableArray2.default)(starts)) + 1;
-  if (estimatedTemplateLength >= 0) (0, _forEach.default)(matedRecords).call(matedRecords, function (r) {
-    if (r.templateLength !== undefined) throw new CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
-    r.templateLength = estimatedTemplateLength;
-  });
 }
 /**
  * @private
@@ -83,746 +82,446 @@ function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumbe
  * @param {CramRecord} thisRecord
  * @param {CramRecord} mateRecord
  */
-
-
 function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
-  // this just estimates the template length by using the simple (non-gapped) end coordinate of each
-  // read, because gapping in the alignment doesn't mean the template is longer or shorter
-  var start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
-  var end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
-  var lengthEstimate = end - start + 1;
-  thisRecord.templateLength = lengthEstimate;
-  mateRecord.templateLength = lengthEstimate;
+    // this just estimates the template length by using the simple (non-gapped) end coordinate of each
+    // read, because gapping in the alignment doesn't mean the template is longer or shorter
+    var start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
+    var end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
+    var lengthEstimate = end - start + 1;
+    thisRecord.templateLength = lengthEstimate;
+    mateRecord.templateLength = lengthEstimate;
 }
 /**
  * @private establishes a mate-pair relationship between two records in the same slice.
  * CRAM compresses mate-pair relationships between records in the same slice down into
  * just one record having the index in the slice of its mate
  */
-
-
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
-  if (!mateRecord) throw new CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
-  var complicatedMultiSegment = !!(mateRecord.mate || mateRecord.mateRecordNumber !== undefined && mateRecord.mateRecordNumber !== currentRecordNumber); // Deal with lossy read names
-
-  if (!thisRecord.readName) {
-    thisRecord.readName = String(thisRecord.uniqueId);
-    mateRecord.readName = thisRecord.readName;
-  }
-
-  thisRecord.mate = {
-    sequenceId: mateRecord.sequenceId,
-    alignmentStart: mateRecord.alignmentStart,
-    uniqueId: mateRecord.uniqueId
-  };
-  if (mateRecord.readName) thisRecord.mate.readName = mateRecord.readName; // the mate record might have its own mate pointer, if this is some kind of
-  // multi-segment (more than paired) scheme, so only relate that one back to this one
-  // if it does not have any other relationship
-
-  if (!mateRecord.mate && mateRecord.mateRecordNumber === undefined) {
-    mateRecord.mate = {
-      sequenceId: thisRecord.sequenceId,
-      alignmentStart: thisRecord.alignmentStart,
-      uniqueId: thisRecord.uniqueId
+    if (!mateRecord) {
+        throw new errors_1.CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
+    }
+    var complicatedMultiSegment = !!(mateRecord.mate ||
+        (mateRecord.mateRecordNumber !== undefined &&
+            mateRecord.mateRecordNumber !== currentRecordNumber));
+    // Deal with lossy read names
+    if (!thisRecord.readName) {
+        thisRecord.readName = String(thisRecord.uniqueId);
+        mateRecord.readName = thisRecord.readName;
+    }
+    thisRecord.mate = {
+        sequenceId: mateRecord.sequenceId,
+        alignmentStart: mateRecord.alignmentStart,
+        uniqueId: mateRecord.uniqueId,
     };
-    if (thisRecord.readName) mateRecord.mate.readName = thisRecord.readName;
-  } // make sure the proper flags and cramFlags are set on both records
-  // paired
-
-
-  thisRecord.flags |= Constants.BAM_FPAIRED; // set mate unmapped if needed
-
-  if ((0, _flags.default)(mateRecord) & Constants.BAM_FUNMAP) {
-    thisRecord.flags |= Constants.BAM_FMUNMAP; // thisRecord.templateLength = 0
-  }
-
-  if ((0, _flags.default)(thisRecord) & Constants.BAM_FUNMAP) {
-    // thisRecord.templateLength = 0
-    mateRecord.flags |= Constants.BAM_FMUNMAP;
-  } // set mate reversed if needed
-
-
-  if ((0, _flags.default)(mateRecord) & Constants.BAM_FREVERSE) {
-    thisRecord.flags |= Constants.BAM_FMREVERSE;
-  }
-
-  if ((0, _flags.default)(thisRecord) & Constants.BAM_FREVERSE) {
-    mateRecord.flags |= Constants.BAM_FMREVERSE;
-  }
-
-  if (thisRecord.templateLength === undefined) {
-    if (complicatedMultiSegment) calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord);else calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord);
-  } // delete this last because it's used by the
-  // complicated template length estimation
-
-
-  delete thisRecord.mateRecordNumber;
+    if (mateRecord.readName) {
+        thisRecord.mate.readName = mateRecord.readName;
+    }
+    // the mate record might have its own mate pointer, if this is some kind of
+    // multi-segment (more than paired) scheme, so only relate that one back to this one
+    // if it does not have any other relationship
+    if (!mateRecord.mate && mateRecord.mateRecordNumber === undefined) {
+        mateRecord.mate = {
+            sequenceId: thisRecord.sequenceId,
+            alignmentStart: thisRecord.alignmentStart,
+            uniqueId: thisRecord.uniqueId,
+        };
+        if (thisRecord.readName) {
+            mateRecord.mate.readName = thisRecord.readName;
+        }
+    }
+    // make sure the proper flags and cramFlags are set on both records
+    // paired
+    thisRecord.flags |= constants_1.default.BAM_FPAIRED;
+    // set mate unmapped if needed
+    if (mateRecord.flags & constants_1.default.BAM_FUNMAP) {
+        thisRecord.flags |= constants_1.default.BAM_FMUNMAP;
+        // thisRecord.templateLength = 0
+    }
+    if (thisRecord.flags & constants_1.default.BAM_FUNMAP) {
+        // thisRecord.templateLength = 0
+        mateRecord.flags |= constants_1.default.BAM_FMUNMAP;
+    }
+    // set mate reversed if needed
+    if (mateRecord.flags & constants_1.default.BAM_FREVERSE) {
+        thisRecord.flags |= constants_1.default.BAM_FMREVERSE;
+    }
+    if (thisRecord.flags & constants_1.default.BAM_FREVERSE) {
+        mateRecord.flags |= constants_1.default.BAM_FMREVERSE;
+    }
+    if (thisRecord.templateLength === undefined) {
+        if (complicatedMultiSegment) {
+            calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord);
+        }
+        else {
+            calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord);
+        }
+    }
+    // delete this last because it's used by the
+    // complicated template length estimation
+    delete thisRecord.mateRecordNumber;
 }
-
-var CramSlice =
-/*#__PURE__*/
-function () {
-  function CramSlice(container, position) {
-    (0, _classCallCheck2.default)(this, CramSlice);
-    this.container = container;
-    this.file = container.file;
-    this.containerPosition = position;
-  } // memoize
-
-
-  (0, _createClass2.default)(CramSlice, [{
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee() {
-        var sectionParsers, containerHeader, header;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.file.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context.sent;
-                _context.next = 5;
-                return this.container.getHeader();
-
-              case 5:
-                containerHeader = _context.sent;
-                _context.next = 8;
-                return this.file.readBlock(containerHeader._endPosition + this.containerPosition);
-
-              case 8:
-                header = _context.sent;
-
-                if (!(header.contentType === 'MAPPED_SLICE_HEADER')) {
-                  _context.next = 13;
-                  break;
-                }
-
-                header.content = parseItem(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
-                _context.next = 18;
-                break;
-
-              case 13:
-                if (!(header.contentType === 'UNMAPPED_SLICE_HEADER')) {
-                  _context.next = 17;
-                  break;
-                }
-
-                header.content = parseItem(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
-                _context.next = 18;
-                break;
-
-              case 17:
-                throw new CramMalformedError("error reading slice header block, invalid content type ".concat(header._contentType));
-
-              case 18:
-                return _context.abrupt("return", header);
-
-              case 19:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }() // memoize
-
-  }, {
-    key: "getBlocks",
-    value: function () {
-      var _getBlocks = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        var header, blockPosition, blocks, i;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.getHeader();
-
-              case 2:
-                header = _context2.sent;
-                // read all the blocks into memory and store them
-                blockPosition = header._endPosition;
-                blocks = new Array(header.content.numBlocks);
-                i = 0;
-
-              case 6:
-                if (!(i < blocks.length)) {
-                  _context2.next = 14;
-                  break;
-                }
-
-                _context2.next = 9;
-                return this.file.readBlock(blockPosition);
-
-              case 9:
-                blocks[i] = _context2.sent;
-                blockPosition = blocks[i]._endPosition;
-
-              case 11:
-                i += 1;
-                _context2.next = 6;
-                break;
-
-              case 14:
-                return _context2.abrupt("return", blocks);
-
-              case 15:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getBlocks() {
-        return _getBlocks.apply(this, arguments);
-      }
-
-      return getBlocks;
-    }() // no memoize
-
-  }, {
-    key: "getCoreDataBlock",
-    value: function () {
-      var _getCoreDataBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        var blocks;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.getBlocks();
-
-              case 2:
-                blocks = _context3.sent;
-                return _context3.abrupt("return", blocks[0]);
-
-              case 4:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getCoreDataBlock() {
-        return _getCoreDataBlock.apply(this, arguments);
-      }
-
-      return getCoreDataBlock;
-    }() // memoize
-
-  }, {
-    key: "_getBlocksContentIdIndex",
-    value: function () {
-      var _getBlocksContentIdIndex2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee4() {
-        var blocks, blocksByContentId;
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.getBlocks();
-
-              case 2:
-                blocks = _context4.sent;
-                blocksByContentId = {};
-                (0, _forEach.default)(blocks).call(blocks, function (block) {
-                  if (block.contentType === 'EXTERNAL_DATA') {
-                    blocksByContentId[block.contentId] = block;
-                  }
-                });
-                return _context4.abrupt("return", blocksByContentId);
-
-              case 6:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function _getBlocksContentIdIndex() {
-        return _getBlocksContentIdIndex2.apply(this, arguments);
-      }
-
-      return _getBlocksContentIdIndex;
-    }()
-  }, {
-    key: "getBlockByContentId",
-    value: function () {
-      var _getBlockByContentId = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee5(id) {
-        var blocksByContentId;
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this._getBlocksContentIdIndex();
-
-              case 2:
-                blocksByContentId = _context5.sent;
-                return _context5.abrupt("return", blocksByContentId[id]);
-
-              case 4:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getBlockByContentId(_x) {
-        return _getBlockByContentId.apply(this, arguments);
-      }
-
-      return getBlockByContentId;
-    }()
-  }, {
-    key: "getReferenceRegion",
-    value: function () {
-      var _getReferenceRegion = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee6() {
-        var sliceHeader, compressionScheme, refBlock, seq;
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.getHeader();
-
-              case 2:
-                sliceHeader = _context6.sent.content;
-
-                if (!(sliceHeader.refSeqId < 0)) {
-                  _context6.next = 5;
-                  break;
-                }
-
-                return _context6.abrupt("return", undefined);
-
-              case 5:
-                _context6.next = 7;
-                return this.container.getCompressionScheme();
-
-              case 7:
-                compressionScheme = _context6.sent;
-
-                if (!(sliceHeader.refBaseBlockId >= 0)) {
-                  _context6.next = 15;
-                  break;
-                }
-
-                refBlock = this.getBlockByContentId(sliceHeader.refBaseBlockId);
-
-                if (refBlock) {
-                  _context6.next = 12;
-                  break;
-                }
-
-                throw new CramMalformedError('embedded reference specified, but reference block does not exist');
-
-              case 12:
-                if (!(sliceHeader.span > refBlock.uncompressedSize)) {
-                  _context6.next = 14;
-                  break;
-                }
-
-                throw new CramMalformedError('Embedded reference is too small');
-
-              case 14:
-                return _context6.abrupt("return", {
-                  seq: refBlock.data.toString('utf8'),
-                  start: sliceHeader.refSeqStart,
-                  end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
-                  span: sliceHeader.refSeqSpan
-                });
-
-              case 15:
-                if (!(compressionScheme.referenceRequired || this.file.fetchReferenceSequenceCallback)) {
-                  _context6.next = 24;
-                  break;
-                }
-
-                if (this.file.fetchReferenceSequenceCallback) {
-                  _context6.next = 18;
-                  break;
-                }
-
-                throw new Error('reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence');
-
-              case 18:
-                _context6.next = 20;
-                return this.file.fetchReferenceSequenceCallback(sliceHeader.refSeqId, sliceHeader.refSeqStart, sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1);
-
-              case 20:
-                seq = _context6.sent;
-
-                if (!(seq.length !== sliceHeader.refSeqSpan)) {
-                  _context6.next = 23;
-                  break;
-                }
-
-                throw new CramArgumentError('seqFetch callback returned a reference sequence of the wrong length');
-
-              case 23:
-                return _context6.abrupt("return", {
-                  seq: seq,
-                  start: sliceHeader.refSeqStart,
-                  end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
-                  span: sliceHeader.refSeqSpan
-                });
-
-              case 24:
-                return _context6.abrupt("return", undefined);
-
-              case 25:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function getReferenceRegion() {
-        return _getReferenceRegion.apply(this, arguments);
-      }
-
-      return getReferenceRegion;
-    }()
-  }, {
-    key: "getAllRecords",
-    value: function getAllRecords() {
-      return this.getRecords(function () {
-        return true;
-      });
+var CramSlice = /** @class */ (function () {
+    function CramSlice(container, position) {
+        this.container = container;
+        this.file = container.file;
+        this.containerPosition = position;
     }
-  }, {
-    key: "_fetchRecords",
-    value: function () {
-      var _fetchRecords2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee7() {
-        var _this = this;
-
-        var _ref, majorVersion, compressionScheme, sliceHeader, blocksByContentId, refRegion, _context7, _context8, _context9, _context10, _context11, seq, start, end, seqMd5, storedMd5, coreDataBlock, cursors, decodeDataSeries, records, i, _i, mateRecordNumber;
-
-        return _regenerator.default.wrap(function _callee7$(_context12) {
-          while (1) {
-            switch (_context12.prev = _context12.next) {
-              case 0:
-                _context12.next = 2;
-                return this.file.getDefinition();
-
-              case 2:
-                _ref = _context12.sent;
-                majorVersion = _ref.majorVersion;
-                _context12.next = 6;
-                return this.container.getCompressionScheme();
-
-              case 6:
-                compressionScheme = _context12.sent;
-                _context12.next = 9;
-                return this.getHeader();
-
-              case 9:
-                sliceHeader = _context12.sent;
-                _context12.next = 12;
-                return this._getBlocksContentIdIndex();
-
-              case 12:
-                blocksByContentId = _context12.sent;
-
-                if (!(majorVersion > 1 && this.file.options.checkSequenceMD5 && sliceHeader.content.refSeqId >= 0 && sliceHeader.content.md5.join('') !== '0000000000000000')) {
-                  _context12.next = 23;
-                  break;
-                }
-
-                _context12.next = 16;
-                return this.getReferenceRegion();
-
-              case 16:
-                refRegion = _context12.sent;
-
-                if (!refRegion) {
-                  _context12.next = 23;
-                  break;
-                }
-
-                seq = refRegion.seq, start = refRegion.start, end = refRegion.end;
-                seqMd5 = sequenceMD5(seq);
-                storedMd5 = (0, _map.default)(_context7 = sliceHeader.content.md5).call(_context7, function (byte) {
-                  return (byte < 16 ? '0' : '') + byte.toString(16);
-                }).join('');
-
-                if (!(seqMd5 !== storedMd5)) {
-                  _context12.next = 23;
-                  break;
+    // memoize
+    CramSlice.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, containerHeader, header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.file.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        return [4 /*yield*/, this.container.getHeader()];
+                    case 2:
+                        containerHeader = _a.sent();
+                        return [4 /*yield*/, this.file.readBlock(containerHeader._endPosition + this.containerPosition)];
+                    case 3:
+                        header = _a.sent();
+                        if (header.contentType === 'MAPPED_SLICE_HEADER') {
+                            header.content = (0, util_1.parseItem)(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
+                        }
+                        else if (header.contentType === 'UNMAPPED_SLICE_HEADER') {
+                            header.content = (0, util_1.parseItem)(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
+                        }
+                        else {
+                            throw new errors_1.CramMalformedError("error reading slice header block, invalid content type ".concat(header._contentType));
+                        }
+                        return [2 /*return*/, header];
                 }
-
-                throw new CramMalformedError((0, _concat.default)(_context8 = (0, _concat.default)(_context9 = (0, _concat.default)(_context10 = (0, _concat.default)(_context11 = "MD5 checksum reference mismatch for ref ".concat(sliceHeader.content.refSeqId, " pos ")).call(_context11, start, "..")).call(_context10, end, ". recorded MD5: ")).call(_context9, storedMd5, ", calculated MD5: ")).call(_context8, seqMd5));
-
-              case 23:
-                _context12.next = 25;
-                return this.getCoreDataBlock();
-
-              case 25:
-                coreDataBlock = _context12.sent;
-                cursors = {
-                  lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
-                  coreBlock: {
-                    bitPosition: 7,
-                    bytePosition: 0
-                  },
-                  externalBlocks: {
-                    getCursor: function getCursor(contentId) {
-                      if (!this[contentId]) this[contentId] = {
-                        bitPosition: 7,
-                        bytePosition: 0
-                      };
-                      return this[contentId];
-                    }
-                  }
-                };
-
-                decodeDataSeries = function decodeDataSeries(dataSeriesName) {
-                  var codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
-                  if (!codec) throw new CramMalformedError("no codec defined for ".concat(dataSeriesName, " data series")); // console.log(dataSeriesName, Object.getPrototypeOf(codec))
-
-                  return codec.decode(_this, coreDataBlock, blocksByContentId, cursors);
-                };
-
-                records = new Array(sliceHeader.content.numRecords);
-                i = 0;
-
-              case 30:
-                if (!(i < records.length)) {
-                  _context12.next = 48;
-                  break;
+            });
+        });
+    };
+    // memoize
+    CramSlice.prototype.getBlocks = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header, blockPosition, blocks, i, _a, _b;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()
+                        // read all the blocks into memory and store them
+                    ];
+                    case 1:
+                        header = _c.sent();
+                        blockPosition = header._endPosition;
+                        blocks = new Array(header.content.numBlocks);
+                        i = 0;
+                        _c.label = 2;
+                    case 2:
+                        if (!(i < blocks.length)) return [3 /*break*/, 5];
+                        _a = blocks;
+                        _b = i;
+                        return [4 /*yield*/, this.file.readBlock(blockPosition)];
+                    case 3:
+                        _a[_b] = _c.sent();
+                        blockPosition = blocks[i]._endPosition;
+                        _c.label = 4;
+                    case 4:
+                        i += 1;
+                        return [3 /*break*/, 2];
+                    case 5: return [2 /*return*/, blocks];
                 }
-
-                _context12.prev = 31;
-                records[i] = decodeRecord(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
-                records[i].uniqueId = sliceHeader.contentPosition + sliceHeader.content.recordCounter + i + 1;
-                _context12.next = 45;
-                break;
-
-              case 36:
-                _context12.prev = 36;
-                _context12.t0 = _context12["catch"](31);
-
-                if (!(_context12.t0 instanceof CramBufferOverrunError)) {
-                  _context12.next = 44;
-                  break;
+            });
+        });
+    };
+    // no memoize
+    CramSlice.prototype.getCoreDataBlock = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var blocks;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getBlocks()
+                        // the core data block is always the first block in the slice
+                    ];
+                    case 1:
+                        blocks = _a.sent();
+                        // the core data block is always the first block in the slice
+                        return [2 /*return*/, blocks[0]];
                 }
-
-                console.warn('read attempted beyond end of buffer, file seems truncated.');
-                records = (0, _filter.default)(records).call(records, function (r) {
-                  return !!r;
-                });
-                return _context12.abrupt("break", 48);
-
-              case 44:
-                throw _context12.t0;
-
-              case 45:
-                i += 1;
-                _context12.next = 30;
-                break;
-
-              case 48:
-                // interpret `recordsToNextFragment` attributes to make standard `mate` objects
-                // Resolve mate pair cross-references between records in this slice
-                for (_i = 0; _i < records.length; _i += 1) {
-                  mateRecordNumber = records[_i].mateRecordNumber;
-                  if (mateRecordNumber >= 0) associateIntraSliceMate(records, _i, records[_i], records[mateRecordNumber]);
+            });
+        });
+    };
+    // memoize
+    CramSlice.prototype._getBlocksContentIdIndex = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var blocks, blocksByContentId;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getBlocks()];
+                    case 1:
+                        blocks = _a.sent();
+                        blocksByContentId = {};
+                        blocks.forEach(function (block) {
+                            if (block.contentType === 'EXTERNAL_DATA') {
+                                blocksByContentId[block.contentId] = block;
+                            }
+                        });
+                        return [2 /*return*/, blocksByContentId];
                 }
-
-                return _context12.abrupt("return", records);
-
-              case 50:
-              case "end":
-                return _context12.stop();
-            }
-          }
-        }, _callee7, this, [[31, 36]]);
-      }));
-
-      function _fetchRecords() {
-        return _fetchRecords2.apply(this, arguments);
-      }
-
-      return _fetchRecords;
-    }()
-  }, {
-    key: "getRecords",
-    value: function () {
-      var _getRecords = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee9(filterFunction) {
-        var _context13,
-            _this2 = this;
-
-        var cacheKey, recordsPromise, records, sliceHeader, _context14, singleRefId, _compressionScheme, refRegions, i, seqId, refRegion, end, _i2, _seqId, _refRegion;
-
-        return _regenerator.default.wrap(function _callee9$(_context16) {
-          while (1) {
-            switch (_context16.prev = _context16.next) {
-              case 0:
-                // fetch the features if necessary, using the file-level feature cache
-                cacheKey = this.container.filePosition + this.containerPosition;
-                recordsPromise = this.file.featureCache.get(cacheKey);
-
-                if (!recordsPromise) {
-                  recordsPromise = this._fetchRecords();
-                  this.file.featureCache.set(cacheKey, recordsPromise);
+            });
+        });
+    };
+    CramSlice.prototype.getBlockByContentId = function (id) {
+        return __awaiter(this, void 0, void 0, function () {
+            var blocksByContentId;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this._getBlocksContentIdIndex()];
+                    case 1:
+                        blocksByContentId = _a.sent();
+                        return [2 /*return*/, blocksByContentId[id]];
                 }
-
-                _context16.t0 = _filter.default;
-                _context16.next = 6;
-                return recordsPromise;
-
-              case 6:
-                _context16.t1 = _context13 = _context16.sent;
-                _context16.t2 = _context13;
-                _context16.t3 = filterFunction;
-                records = (0, _context16.t0)(_context16.t1).call(_context16.t2, _context16.t3);
-
-                if (!(records.length && this.file.fetchReferenceSequenceCallback)) {
-                  _context16.next = 24;
-                  break;
+            });
+        });
+    };
+    CramSlice.prototype.getReferenceRegion = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var sliceHeader, compressionScheme, refBlock, seq;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()];
+                    case 1:
+                        sliceHeader = (_a.sent()).content;
+                        if (sliceHeader.refSeqId < 0) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [4 /*yield*/, this.container.getCompressionScheme()
+                            // console.log(JSON.stringify(sliceHeader, null, '  '))
+                        ];
+                    case 2:
+                        compressionScheme = _a.sent();
+                        // console.log(JSON.stringify(sliceHeader, null, '  '))
+                        if (sliceHeader.refBaseBlockId >= 0) {
+                            refBlock = this.getBlockByContentId(sliceHeader.refBaseBlockId);
+                            if (!refBlock) {
+                                throw new errors_1.CramMalformedError('embedded reference specified, but reference block does not exist');
+                            }
+                            if (sliceHeader.span > refBlock.uncompressedSize) {
+                                throw new errors_1.CramMalformedError('Embedded reference is too small');
+                            }
+                            return [2 /*return*/, {
+                                    seq: refBlock.data.toString('utf8'),
+                                    start: sliceHeader.refSeqStart,
+                                    end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
+                                    span: sliceHeader.refSeqSpan,
+                                }];
+                        }
+                        if (!(compressionScheme.referenceRequired ||
+                            this.file.fetchReferenceSequenceCallback)) return [3 /*break*/, 4];
+                        if (!this.file.fetchReferenceSequenceCallback) {
+                            throw new Error('reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence');
+                        }
+                        return [4 /*yield*/, this.file.fetchReferenceSequenceCallback(sliceHeader.refSeqId, sliceHeader.refSeqStart, sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1)];
+                    case 3:
+                        seq = _a.sent();
+                        if (seq.length !== sliceHeader.refSeqSpan) {
+                            throw new errors_1.CramArgumentError('seqFetch callback returned a reference sequence of the wrong length');
+                        }
+                        return [2 /*return*/, {
+                                seq: seq,
+                                start: sliceHeader.refSeqStart,
+                                end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
+                                span: sliceHeader.refSeqSpan,
+                            }];
+                    case 4: return [2 /*return*/, undefined];
                 }
-
-                _context16.next = 13;
-                return this.getHeader();
-
-              case 13:
-                sliceHeader = _context16.sent;
-
-                if (!(sliceHeader.content.refSeqId >= 0 || // single-ref slice
-                sliceHeader.content.refSeqId === -2 // multi-ref slice
-                )) {
-                  _context16.next = 24;
-                  break;
+            });
+        });
+    };
+    CramSlice.prototype.getAllRecords = function () {
+        return this.getRecords(function () { return true; });
+    };
+    CramSlice.prototype._fetchRecords = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var majorVersion, compressionScheme, sliceHeader, blocksByContentId, refRegion, seq, start, end, seqMd5, storedMd5, coreDataBlock, cursors, decodeDataSeries, records, i, i, mateRecordNumber;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.file.getDefinition()];
+                    case 1:
+                        majorVersion = (_a.sent()).majorVersion;
+                        return [4 /*yield*/, this.container.getCompressionScheme()];
+                    case 2:
+                        compressionScheme = _a.sent();
+                        return [4 /*yield*/, this.getHeader()];
+                    case 3:
+                        sliceHeader = _a.sent();
+                        return [4 /*yield*/, this._getBlocksContentIdIndex()
+                            // check MD5 of reference if available
+                        ];
+                    case 4:
+                        blocksByContentId = _a.sent();
+                        if (!(majorVersion > 1 &&
+                            this.file.options.checkSequenceMD5 &&
+                            sliceHeader.content.refSeqId >= 0 &&
+                            sliceHeader.content.md5.join('') !== '0000000000000000')) return [3 /*break*/, 6];
+                        return [4 /*yield*/, this.getReferenceRegion()];
+                    case 5:
+                        refRegion = _a.sent();
+                        if (refRegion) {
+                            seq = refRegion.seq, start = refRegion.start, end = refRegion.end;
+                            seqMd5 = (0, util_1.sequenceMD5)(seq);
+                            storedMd5 = sliceHeader.content.md5
+                                .map(function (byte) { return (byte < 16 ? '0' : '') + byte.toString(16); })
+                                .join('');
+                            if (seqMd5 !== storedMd5) {
+                                throw new errors_1.CramMalformedError("MD5 checksum reference mismatch for ref ".concat(sliceHeader.content.refSeqId, " pos ").concat(start, "..").concat(end, ". recorded MD5: ").concat(storedMd5, ", calculated MD5: ").concat(seqMd5));
+                            }
+                        }
+                        _a.label = 6;
+                    case 6: return [4 /*yield*/, this.getCoreDataBlock()];
+                    case 7:
+                        coreDataBlock = _a.sent();
+                        cursors = {
+                            lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
+                            coreBlock: { bitPosition: 7, bytePosition: 0 },
+                            externalBlocks: {
+                                getCursor: function (contentId) {
+                                    if (!this[contentId]) {
+                                        this[contentId] = { bitPosition: 7, bytePosition: 0 };
+                                    }
+                                    return this[contentId];
+                                },
+                            },
+                        };
+                        decodeDataSeries = function (dataSeriesName) {
+                            var codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
+                            if (!codec) {
+                                throw new errors_1.CramMalformedError("no codec defined for ".concat(dataSeriesName, " data series"));
+                            }
+                            // console.log(dataSeriesName, Object.getPrototypeOf(codec))
+                            return codec.decode(_this, coreDataBlock, blocksByContentId, cursors);
+                        };
+                        records = new Array(sliceHeader.content.numRecords);
+                        for (i = 0; i < records.length; i += 1) {
+                            try {
+                                records[i] = (0, decodeRecord_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
+                                records[i].uniqueId =
+                                    sliceHeader.contentPosition +
+                                        sliceHeader.content.recordCounter +
+                                        i +
+                                        1;
+                            }
+                            catch (e) {
+                                if (e instanceof errors_1.CramBufferOverrunError) {
+                                    console.warn('read attempted beyond end of buffer, file seems truncated.');
+                                    records = records.filter(function (r) { return !!r; });
+                                    break;
+                                }
+                                else {
+                                    throw e;
+                                }
+                            }
+                        }
+                        // interpret `recordsToNextFragment` attributes to make standard `mate` objects
+                        // Resolve mate pair cross-references between records in this slice
+                        for (i = 0; i < records.length; i += 1) {
+                            mateRecordNumber = records[i].mateRecordNumber;
+                            if (mateRecordNumber >= 0) {
+                                associateIntraSliceMate(records, i, records[i], records[mateRecordNumber]);
+                            }
+                        }
+                        return [2 /*return*/, records];
                 }
-
-                singleRefId = sliceHeader.content.refSeqId >= 0 ? sliceHeader.content.refSeqId : undefined;
-                _context16.next = 18;
-                return this.container.getCompressionScheme();
-
-              case 18:
-                _compressionScheme = _context16.sent;
-                refRegions = {}; // seqId => { start, end, seq }
-                // iterate over the records to find the spans of the reference sequences we need to fetch
-
-                for (i = 0; i < records.length; i += 1) {
-                  seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
-                  refRegion = refRegions[seqId];
-
-                  if (!refRegion) {
-                    refRegion = {
-                      id: seqId,
-                      start: records[i].alignmentStart,
-                      end: -Infinity
-                    };
-                    refRegions[seqId] = refRegion;
-                  }
-
-                  end = records[i].alignmentStart + (records[i].lengthOnRef || records[i].readLength) - 1;
-                  if (end > refRegion.end) refRegion.end = end;
-                  if (records[i].alignmentStart < refRegion.start) refRegion.start = records[i].alignmentStart;
-                } // fetch the `seq` for all of the ref regions
-
-
-                _context16.next = 23;
-                return _promise.default.all((0, _map.default)(_context14 = (0, _values.default)(refRegions)).call(_context14,
-                /*#__PURE__*/
-                function () {
-                  var _ref2 = (0, _asyncToGenerator2.default)(
-                  /*#__PURE__*/
-                  _regenerator.default.mark(function _callee8(refRegion) {
-                    return _regenerator.default.wrap(function _callee8$(_context15) {
-                      while (1) {
-                        switch (_context15.prev = _context15.next) {
-                          case 0:
-                            if (!(refRegion.id !== -1 && refRegion.start <= refRegion.end)) {
-                              _context15.next = 4;
-                              break;
+            });
+        });
+    };
+    CramSlice.prototype.getRecords = function (filterFunction) {
+        return __awaiter(this, void 0, void 0, function () {
+            var cacheKey, recordsPromise, records, sliceHeader, singleRefId, compressionScheme, refRegions, i, seqId, refRegion, end, i, seqId, refRegion;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        cacheKey = this.container.filePosition + this.containerPosition;
+                        recordsPromise = this.file.featureCache.get(cacheKey);
+                        if (!recordsPromise) {
+                            recordsPromise = this._fetchRecords();
+                            this.file.featureCache.set(cacheKey, recordsPromise);
+                        }
+                        return [4 /*yield*/, recordsPromise];
+                    case 1:
+                        records = (_a.sent()).filter(filterFunction);
+                        if (!(records.length && this.file.fetchReferenceSequenceCallback)) return [3 /*break*/, 5];
+                        return [4 /*yield*/, this.getHeader()];
+                    case 2:
+                        sliceHeader = _a.sent();
+                        if (!(sliceHeader.content.refSeqId >= 0 || // single-ref slice
+                            sliceHeader.content.refSeqId === -2) // multi-ref slice
+                        ) return [3 /*break*/, 5]; // multi-ref slice
+                        singleRefId = sliceHeader.content.refSeqId >= 0
+                            ? sliceHeader.content.refSeqId
+                            : undefined;
+                        return [4 /*yield*/, this.container.getCompressionScheme()];
+                    case 3:
+                        compressionScheme = _a.sent();
+                        refRegions = {} // seqId => { start, end, seq }
+                        ;
+                        // iterate over the records to find the spans of the reference sequences we need to fetch
+                        for (i = 0; i < records.length; i += 1) {
+                            seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                            refRegion = refRegions[seqId];
+                            if (!refRegion) {
+                                refRegion = {
+                                    id: seqId,
+                                    start: records[i].alignmentStart,
+                                    end: -Infinity,
+                                };
+                                refRegions[seqId] = refRegion;
+                            }
+                            end = records[i].alignmentStart +
+                                (records[i].lengthOnRef || records[i].readLength) -
+                                1;
+                            if (end > refRegion.end) {
+                                refRegion.end = end;
+                            }
+                            if (records[i].alignmentStart < refRegion.start) {
+                                refRegion.start = records[i].alignmentStart;
                             }
-
-                            _context15.next = 3;
-                            return _this2.file.fetchReferenceSequenceCallback(refRegion.id, refRegion.start, refRegion.end);
-
-                          case 3:
-                            refRegion.seq = _context15.sent;
-
-                          case 4:
-                          case "end":
-                            return _context15.stop();
                         }
-                      }
-                    }, _callee8);
-                  }));
-
-                  return function (_x3) {
-                    return _ref2.apply(this, arguments);
-                  };
-                }()));
-
-              case 23:
-                // now decorate all the records with them
-                for (_i2 = 0; _i2 < records.length; _i2 += 1) {
-                  _seqId = singleRefId !== undefined ? singleRefId : records[_i2].sequenceId;
-                  _refRegion = refRegions[_seqId];
-
-                  if (_refRegion && _refRegion.seq) {
-                    records[_i2].addReferenceSequence(_refRegion, _compressionScheme);
-                  }
+                        // fetch the `seq` for all of the ref regions
+                        return [4 /*yield*/, Promise.all(Object.values(refRegions).map(function (refRegion) { return __awaiter(_this, void 0, void 0, function () {
+                                var _a;
+                                return __generator(this, function (_b) {
+                                    switch (_b.label) {
+                                        case 0:
+                                            if (!(refRegion.id !== -1 && refRegion.start <= refRegion.end)) return [3 /*break*/, 2];
+                                            _a = refRegion;
+                                            return [4 /*yield*/, this.file.fetchReferenceSequenceCallback(refRegion.id, refRegion.start, refRegion.end)];
+                                        case 1:
+                                            _a.seq = _b.sent();
+                                            _b.label = 2;
+                                        case 2: return [2 /*return*/];
+                                    }
+                                });
+                            }); }))
+                            // now decorate all the records with them
+                        ];
+                    case 4:
+                        // fetch the `seq` for all of the ref regions
+                        _a.sent();
+                        // now decorate all the records with them
+                        for (i = 0; i < records.length; i += 1) {
+                            seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                            refRegion = refRegions[seqId];
+                            if (refRegion && refRegion.seq) {
+                                records[i].addReferenceSequence(refRegion, compressionScheme);
+                            }
+                        }
+                        _a.label = 5;
+                    case 5: return [2 /*return*/, records];
                 }
-
-              case 24:
-                return _context16.abrupt("return", records);
-
-              case 25:
-              case "end":
-                return _context16.stop();
-            }
-          }
-        }, _callee9, this);
-      }));
-
-      function getRecords(_x2) {
-        return _getRecords.apply(this, arguments);
-      }
-
-      return getRecords;
-    }()
-  }]);
-  return CramSlice;
-}(); // memoize several methods in the class for performance
-
-
-(0, _forEach.default)(_context17 = 'getHeader getBlocks _getBlocksContentIdIndex'.split(' ')).call(_context17, function (method) {
-  return tinyMemoize(CramSlice, method);
-});
-module.exports = CramSlice;
+            });
+        });
+    };
+    return CramSlice;
+}());
+exports.default = CramSlice;
+// memoize several methods in the class for performance
+'getHeader getBlocks _getBlocksContentIdIndex'
+    .split(' ')
+    .forEach(function (method) { return (0, util_1.tinyMemoize)(CramSlice, method); });
+//# sourceMappingURL=index.js.map